Owen Paterson (foreground) stops short of suggesting that the pilot culls have been effective, saying only that 'the pilot has been safe and humane'. Photograph: Rex

The badger cull in Somerset has failed to reach the government's target despite being extended from six to nine weeks. Environment secretary Owen Paterson informed parliament on Tuesday that the additional night-time shoots had killed just 90 more badgers, meaning about 65% of the estimated population had been eradicated.

The government's original policy was to cull a minimum of 70% of badgers in a maximum of six weeks, to minimise the risk of fleeing badgers spreading tuberculosis (TB) more widely and increasing infections in cattle, rather than reducing them. Bovine TB is rising and led to the slaughter of 28,000 cattle in England in 2012.

The pilot badger culls in Somerset and Gloucestershire were intended to test whether the shooting of free-running badgers at night is effective, safe and humane.

In Paterson's written statement to MPs, he stops short of suggesting that the pilot culls have been effective, stating only: "Current indications suggest that the pilot has been safe and humane." He said the 65% cull rate would "deliver clear disease benefits" based on advice from chief veterinary officer Nigel Gibbens.

However, that advice has been contested by the UK's leading badger experts, including Professor Rosie Woodroffe, a key member of the team that conducted a landmark decade-long badger culling trial. "The chief vet's advice to carry on culling is based upon a very incomplete view of the available evidence," she says.

"Pushing through this cull extension before the government's own independent expert panel has had a chance to assess the pilots shows just how little Defra [the Department for Environment, Food and Rural Affairs] seems to care about scientific evidence on this matter. TB is a huge problem for cattle farmers, and they deserve better than to be left footing the bill for culling when the likely benefits are diminishing and the costs are spiralling."

In the decade-long trial, which showed an eventual reduction in bovine TB of about 16%, more than 70% badgers were culled in eight-11 days, using the more reliable but more expensive technique of cage-trapping and shooting.

The 65% cull rate in Somerset is based on estimates of the initial badger population that were drastically reduced by the government: from 4,290 in October 2012 to 1,450 in October 2013. Paterson blamed weather and disease and said that badgers had "moved the goalposts" for the cull. This explanation was rejected by experts, who noted that other closely monitored populations had seen no similar decline.

Paterson's statement said it had been difficult to conduct the cull: "I would like to pay tribute to the local farmers and landowners who have undertaken the cull, often in difficult terrain and weather, and often in the face of intimidation by a small minority who are determined to stop this disease control policy."

He also reasserted his determination to persevere: "Achieving our aim of ridding England of bovine TB within 25 years will require long- term solutions and considerable national resolve. This government is committed to tackling the disease in all reservoirs and by all available means."

Maria Eagle, Labour's shadow environment secretary, said: "David Cameron should stop the unscientific mass culling of badgers now that Paterson's misguided policy has clearly failed. Scientists have warned all along that a botched cull is worse than no cull at all. By repeatedly moving the goalposts on his own policy, Paterson has risked the further spread of TB due to prolonged disturbance of local badger populations."